President of the European Council Donald Tusk visits Rome with German Chancellor Angela Merkel and EU institution leaders to discuss Europe's refugee crisis.

Refugees seen during a rescue operation by the Italian navy off the coast of the south of the Italian island of Sicily in 2013.

European Council President Donald Tusk began his two day visit to Rome on Thursday to discuss the refugees crisis and the effect it has had on European countries. He was joined by German Chancellor Angela Merkel and the council leaders.

Italian Prime Minister Matteo Renzi is hosting the first day of talks, followed by Pope Francis on Friday. He fears his country will become the new refugee frontline after the closure of the Balkan route.

As the EU braces for more turbulence notably with next month's "Brexit" referendum in Britain as well as renewed Greek debt talks, Italy is keen to keep the focus on forging a joint plan over refugees.

Renzi is meeting with Merkel, followed by talks with European Commission leader Jean-Claude Juncker, EU Council president Tusk and European Parliament chief Martin Schulz.

From 6:30 pm (1630 GMT) they will hold a conference on the future of the EU, which will take place in the same room in the Capitole where the 1957 Rome Treaty was signed, founding the body that developed into today's 28-nation EU.

With over 28,500 refugees having arrived since January 1, Italy has once again become the principal entry via the Mediterranean, after the controversial EU-Turkey deal and the closure of the Balkan route north.

Refugees rest after disembarking from the British assault ship HMS Bulwark at the Sicilian port of Catania after being rescued at sea, Italy, June 8, 2015. (Reuters Archive)

Rome fears that, unlike previously, Italy will be left hosting masses of new arrivals if, for example, Austria mounts stricter controls at the Brenner pass linking Italy through the Alps to northern Europe.

Threats to the Schengen Treaty on free movement sparked by the refugee crisis were described by Italian Finance Minister Pier Carlo Padoan as "more dangerous than the euro crisis a few years ago".

UN refugee agency spokeswoman in Italy, Carlotta Sami, on Wednesday welcomed the "movement from an emergency approach to a structured approach, making plans and reflecting on (the) integration" of refugees into countries where they arrive.

Rome this week unveiled plans to fingerprint refugees crossing the Mediterranean as soon as they are picked up by rescue boats.

Refugees at the Sicilian harbour of Pozzallo, February 15, 2015. (Reuters Archive)

There have long been tensions with other EU countries over refugees arriving in Italy and travelling north without being registered.

Under the EU's much-criticised Dublin Treaty, asylum claims must be processed by the first country in which refugees arrive.

Italy was warned last year by the European Commission that it must make its registration procedures more efficient.

After Renzi on Thursday, Pope Francis will meet Merkel and the three EU institution leaders on Friday, before making a speech as he is given the EU's Charlemagne prize, which each year honours "an exceptional contribution to European unification."

The Pope, who usually refuses prizes, explained in February that he accepted this one in order to appeal for a "refounding" of the European bloc. In November 2014, he called at the European Parliament for Europe to become a "reference point for humanity."